A Pakistani sailor serving on a Navy vessel participating in war games off the coast of Darwin appears to have jumped ship and was last seen hiding in bushes on the mainland.

Police Superintendent Rob Burgoyne said police were alerted to the incident by a call from the Navy about 4:30am (CST) on Sunday morning.

"A backpack was found in the water which would indicate that the person leaving the ship did know what he was doing at the time and didn't simply fall off the ship," Superintendent Burgoyne said.

He said the sailor was spotted on the mainland in a fairly remote area by a caretaker from a local YMCA.

"He was described as skulking in the bushes, so one can work out from that, probably he didn't want to be found," Superintendent Burgoyne said.

He said the waters the sailor swam through to get to the mainland were known as a crocodile habitat.

"This person is probably lucky that he didn't come across one (crocodile) when he was in the water," Supt Burgoyne said.

The sailor is believed to have made landfall near Talc Head, about 115 kilometres from Darwin by road, on the other side of Darwin Harbour from the city.

"It is fairly bushy, low scrub type, as you would find on the coast, mangroves and there is a beach cliff face sort of thing there as well," Supt Burgoyne said.

Police are using dogs in the search for the sailor, and are being helped by an Australian Navy helicopter.

The navy vessels were taking part in Exercise Kakadu - Australia's largest maritime exercise, with 15 nations from the Asia Pacific taking part this year.

A spokeswoman for Exercise Kakadu said the man was travelling on Pakistani vessel PNS NASR.

She said Exercise Kakadu had not been affected by the incident.

Pakistani sailor faces disciplinary action

Defence adviser to the Pakistan High Commission in Canberra Brigadier Muhammad Asghar said it was too early to say whether the sailor had slipped into the water or jumped, but either way the Pakistani government wanted the man returned to them as soon as possible.

The man would likely face disciplinary action from the Pakistan Navy for "absenting from a place of duty", and if found guilty could face criminal charges and expulsion from the Navy, Brigadier Asghar said*.*

In a statement, the Australian Defence Force (ADF) confirmed the Pakistani sailor had gone missing and they were helping in the efforts to find him.

The ADF said the sailor's personal details would not immediately be released